Following is the path to repeatmasker.pm on my system
/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Tools/RepeatMasker.pm
but when I run my program, the error message comes
RepeatMasker program not found as or not executable
Here is my piece of code which gives this error,
#!/usr/bin/perl
use strict;
use warnings;
use Bio::Seq;
use Bio::Tools::Run::StandAloneBlast;
use Bio::Search::Hit::HitI;
use Bio::Search::Hit::BlastHit;
use Bio::Search::HSP::BlastHSP;
use Bio::Search::HSP::HSPI;
use Bio::SearchIO;
use Bio::Tools::Run::RepeatMasker;
BEGIN {
$ENV{REPEATMASKERDIR} = '/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Tools/';
}
my @params = ("mam" => 1,"noint"=>1);
my $factory = Bio::Tools::Run::RepeatMasker->new(@params);
my $in = Bio::SeqIO->new(-file => "boechera.fasta", -format => 'fasta');
I tried finding RepeatMasker directory by typing
which RepeatMasker
but the error message was
/usr/bin/which: no RepeatMasker in
(/opt/openmpi/1.1.4/bin:/opt/lsfhpc/ego/1.2/linux2.6-glibc2.3-x86_64/etc:/opt/lsfhpc/ego/1.2/linux2.6-glibc2.3-x86_64/bin:/opt/lsfhpc/7.0/linux2.6-glibc2.3-x86_64/etc:/opt/lsfhpc/7.0/linux2.6-glibc2.3-x86_64/bin:/usr/kerberos/bin:/usr/java/jdk1.5.0_07/bin:/share/iNquiry/biotools/bin:/share/iNquiry/bin/lx24-x86:/share/iNquiry/bin/lx24-amd64:/opt/Bio/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/opt/modules/current/bin/:/opt/modules/bin/:/opt/Bio/glimmer/scripts:/opt/Bio/gromacs/bin:/opt/eclipse:/opt/ganglia/bin:/opt/maven/bin:/opt/rocks/bin:/opt/rocks/sbin:/home/vdar/bin)
what should I do?
Thanks
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